The flanking subs did exactly what I would have expected, which was to reduce 15dB ripple in the 100-200Hz region to 6dB ripple. That's a "textbook case" of what to expect. Flanking subs can smooth the range a little lower than 100Hz - usually down to 80Hz and sometimes as low as 60Hz - but below 60-80Hz is where distributed multisubs work best.

As for over-representation in the 100-300Hz range, that's not really something the flanking sub configuration can address. Flanking subs don't usually go that high and even if they did, they will generally add energy rather than cancel it.

And as frequency rises above 200Hz, sound becomes more statistical - a reverberent field - so it tends to become more of an average sound level and not distinct modes. That's where the EQ will become more effective.

...flanking subs don't have to dig deep, they just have to blend with the mains in the 80-200Hz range. So they don't necessarily need to be large. And distributed multisubs - placed further away - can be small and relatively inefficient because the fact that you are using several tends to increase SPL. So you can use relatively small boxes, and that helps when trying to work with the room decor.